Workflow to apply NCR and reference artifact filters and remove zero-carrier sites

broadinstitute / gatk-sv

A structural variation pipeline for short-read sequencing

BSD 3-Clause "New" or "Revised" License

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Workflow to apply NCR and reference artifact filters and remove zero-carrier sites #653

Open epiercehoffman opened 4 months ago

epiercehoffman commented 4 months ago

Updates

Create a standalone WDL for NCR and reference artifact filters. Also removes sites with zero carriers. This script pulls code from the existing NCR calculation in apply_sl_filter.py but applies it independently from genotype filtering to allow for intervening steps like outlier removal and CPX filtering which impact the NCR calculation.

Marked as draft while AoU Phase 2 downstream steps development is ongoing.

mwalker174 commented 2 months ago

We need to have an offline discussion about how to streamline these downstream steps. Not ideal to have two implementations of NCR.